+Open data
-Basic information
Entry | Database: PDB / ID: 2qqn | ||||||
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Title | Neuropilin-1 b1 Domain in Complex with a VEGF-Blocking Fab | ||||||
Components |
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Keywords | SIGNALING PROTEIN / VEGF receptor / semaphorin receptor / Phage-Derived Antibody / Angiogenesis / Developmental protein / Differentiation / Glycoprotein / Heparan sulfate / Membrane / Neurogenesis / Proteoglycan / Secreted / Transmembrane / HORMONE | ||||||
Function / homology | Function and homology information endothelial tip cell fate specification / basal dendrite development / protein localization to early endosome / otic placode development / neurofilament / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / retina vasculature morphogenesis in camera-type eye / regulation of vascular endothelial growth factor receptor signaling pathway / vestibulocochlear nerve structural organization ...endothelial tip cell fate specification / basal dendrite development / protein localization to early endosome / otic placode development / neurofilament / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / retina vasculature morphogenesis in camera-type eye / regulation of vascular endothelial growth factor receptor signaling pathway / vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / postsynapse organization / branchiomotor neuron axon guidance / renal artery morphogenesis / axon extension involved in axon guidance / VEGF-activated neuropilin signaling pathway / negative regulation of axon extension involved in axon guidance / sympathetic neuron projection extension / Neurophilin interactions with VEGF and VEGFR / vascular endothelial growth factor binding / endothelial cell chemotaxis / motor neuron migration / axonogenesis involved in innervation / sympathetic ganglion development / neural crest cell migration involved in autonomic nervous system development / positive regulation of axon extension involved in axon guidance / CHL1 interactions / vascular endothelial growth factor receptor activity / substrate-dependent cell migration, cell extension / semaphorin receptor complex / regulation of vesicle-mediated transport / Signaling by ROBO receptors / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / angiogenesis involved in coronary vascular morphogenesis / hepatocyte growth factor receptor signaling pathway / neuropilin signaling pathway / coronary artery morphogenesis / outflow tract septum morphogenesis / semaphorin receptor activity / CRMPs in Sema3A signaling / commissural neuron axon guidance / motor neuron axon guidance / cell migration involved in sprouting angiogenesis / retinal ganglion cell axon guidance / axonal fasciculation / regulation of Cdc42 protein signal transduction / sprouting angiogenesis / neural crest cell migration / positive regulation of filopodium assembly / artery morphogenesis / branching involved in blood vessel morphogenesis / cellular response to hepatocyte growth factor stimulus / positive regulation of cell migration involved in sprouting angiogenesis / positive chemotaxis / cytokine binding / positive regulation of smooth muscle cell migration / growth factor binding / sorting endosome / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / platelet-derived growth factor receptor signaling pathway / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / vascular endothelial growth factor receptor signaling pathway / coreceptor activity / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / positive regulation of endothelial cell proliferation / GTPase activator activity / positive regulation of endothelial cell migration / Signal transduction by L1 / axon guidance / integrin-mediated signaling pathway / mitochondrial membrane / negative regulation of extrinsic apoptotic signaling pathway / animal organ morphogenesis / neuron migration / response to wounding / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell signaling / heparin binding / cytoplasmic vesicle / postsynaptic membrane / angiogenesis / negative regulation of neuron apoptotic process / Attachment and Entry / positive regulation of ERK1 and ERK2 cascade / receptor complex / early endosome / neuron projection Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Appleton, B.A. / Wiesmann, C. | ||||||
Citation | Journal: Embo J. / Year: 2007 Title: Structural studies of neuropilin/antibody complexes provide insights into semaphorin and VEGF binding Authors: Appleton, B.A. / Wu, P. / Maloney, J. / Yin, J. / Liang, W.C. / Stawicki, S. / Mortara, K. / Bowman, K.K. / Elliott, J.M. / Desmarais, W. / Bazan, J.F. / Bagri, A. / Tessier-Lavigne, M. / ...Authors: Appleton, B.A. / Wu, P. / Maloney, J. / Yin, J. / Liang, W.C. / Stawicki, S. / Mortara, K. / Bowman, K.K. / Elliott, J.M. / Desmarais, W. / Bazan, J.F. / Bagri, A. / Tessier-Lavigne, M. / Koch, A.W. / Wu, Y. / Watts, R.J. / Wiesmann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qqn.cif.gz | 134.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qqn.ent.gz | 102.5 KB | Display | PDB format |
PDBx/mmJSON format | 2qqn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/2qqn ftp://data.pdbj.org/pub/pdb/validation_reports/qq/2qqn | HTTPS FTP |
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-Related structure data
Related structure data | 2qqiC 2qqjC 2qqkC 2qqlC 2qqmC 2qqoC 1kexS 2fjhS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18004.369 Da / Num. of mol.: 1 / Fragment: F5/8 type C 1 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NRP1, NRP, VEGF165R / Production host: Escherichia coli (E. coli) / References: UniProt: O14786 | ||
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#2: Antibody | Mass: 24289.260 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) | ||
#3: Antibody | Mass: 23305.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.77 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop Details: 25% PEG 1500, 4% tert-butanol, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 6, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 39195 / % possible obs: 99 % / Redundancy: 4.4 % / Biso Wilson estimate: 41.1 Å2 / Rsym value: 0.096 / Χ2: 1.014 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 3893 / Rsym value: 0.485 / Χ2: 0.913 / % possible all: 98 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KEX (b1 domain), 2FJH (Fab) Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 8.831 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.243 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.245 Å / Total num. of bins used: 25
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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